How many researchers…?

image of a light bulb

The best thing about being a statistician…

John Tukey

Children’s Mercy Hospital

Image of Children’s Mercy Hospital, Adele Hall Campus

Cleveland Chiropractic

Cleveland Chiropractic College campus

MRI Global

MRI Global building

North Kansas City Hospital

North Kansas City Hospital

Saint Luke’s Hospital

Saint Luke’s Hospital building

Truman Medical Center

Truman Medical Center building

UMKC and KUMC

UMKC and KUMC mascots

New backyard: Russ Waitman

Russ Waitman

i2b2 software

Screenshot of i2b2 software

The database structure behind i2b2

Diagram of i2b2 schema

How many surgeries?

select_surgeries <- 
  "SELECT name_char FROM blueherondata.concept_dimension
     WHERE name_char LIKE '%ectomy%'"     
dbGetQuery(c_connect, select_surgeries) %>%   # Extract records
  use_series(NAME_CHAR) %>%                   # Convert to vector
  strsplit(" ") %>%                           # Split into words
  unlist %>%                                  # Re-convert to vector
  tolower %>%                                 # Force to lower case
  grep("ectomy", ., value=TRUE) %>%           # Toss extraneous words
  gsub("[[:punct:]]", "", .) %>%              # Remove punctuation
  gsub("ectomy.*", "-", .) %>%                # Remove ectomy suffix
  unique %>%                                  # Remove duplicates
  sample(100, replace=FALSE) %>%              # Select 100 random
  sort %>%                                    # Arrange
  paste(collapse=", ")                        # Delimit with commas

How many surgeries?

“acromion-, adenoid-, alveol-, apic-, apico-, arthr-, arytenoid-, astragal-, ather-, burs-, capsul-, carp-, clitor-, coccyg-, crani-, dacryoaden-, dacryocyst-, diaphys-, disarticulationhemipelv-, disk-, diverticul-, endarter-, epididym-, epiglottid-, epiplo-, ethmoid-, fasci-, fistul-, frenul-, ganglion-, gastr-, gingiv-, gloss-, hemigastr-, hemigloss-, hemilamin-, hemilaryng-, hemiphalang-, hemorrhoid-, hepat-, hymen-, hyster-, infundibul-, irid-, labyrinth-, lamin-, lip-, lump-, mucos-, my-, myom-, nephr-, nephroureter-, oophor-, osteophyt-, pannicul-, patell-, phalang-, pharyngolaryng-, phleb-, pleur-, plex-, pneumon-, postadenoid-, postcholecyst-, postgastr-, postlymphaden-, postmastoid-, postpolyp-, postprostat-, postsplen-, prostat-, rectosigmoid-, salping-, salpingoophor-, scler-, segment-, sequestr-, sialoaden-, sigmoid-, sphenoid-, sympath-, synov-, tenon-, tenosynov-, trabecul-, trachel-, trisection-, trisegment-, turbin-, tyl-, tympanomastoid-, umbil-, urethr-, uvul-, vagin-, valv-, vas-, vesicul-, vulv-”

Mei Liu, Acute Kidney Injury

Mei Liu, next to one of her research publications

Requirements needed for mining the electronic health record

Technical requirements

  • Working familiarity with SQL
  • Data wrangling skills

Non-technical requirements

  • Lust for data
  • An interesting backyard

Informatics meetup

Flier for May 23 Informatics meetup

Bibliography